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Genomics and Soft Cheese

You would never guess how many life forms thrive on a cheese. Yet that’s where all the flavour comes from! Steve Labrie explores the microscopic world of cheeses and maps the genes of the bacteria and fungi that proliferate on their surface – all in aid of helping the cheesemaking industry improve its products.

If you were able to shrink yourself and take a walk on a cheese, you would feel like you were trekking through a jungle. Long mushroom filaments litter the surface or hang like lianas, thousands of bacteria of every kind occupy every nook and cranny, millions of spores are released at every moment ... biodiversity on a par with the greatest tropical forests on earth!

Labrie, a researcher at Université Laval’s food mycology laboratory, explores the world of invisible ecosystems. He has developed genetic tools to establish the flora profile of each cheese, to help cheesemakers ensure the consistency of their products.

Maintaining quality and taste is the cheesemaker’s holy grail. Year in, year out, producers habitually absorb losses of 2 to 20% due to imbalances that occasionally affect the microflora.

Hence the importance of Steve Labrie’s work for large cheesemakers, which can be quite costly when cheeses are spoiled.

“Each cheese has its own distinctive microbial flora,” Steve Labrie tells us. “An entire ecosystem lives on a cheese, an ecosystem that gives it its flavour and the character that distinguishes it from all the others.”

“The goal is to perfect our knowledge of the microbial strains that are present in each variety of cheese and ensure that they - and only they - are there every time we manufacture a new batch.”

On hard cheeses, the number of microbial species is relatively limited. For example, the surface of cheddar is dominated by Lactobacilli, bacteria that produce lactic acid, while in a cheese with a mould rind, like Camembert, you can find yeast, Penicillium fungi or Geotricum (responsible for the white rind), lactic bacteria, etc.

Where do all these microbes come from? From the milk, initially, but also the curdling process, during which bacteria are purposely incorporated into milk to transform it.

After that, during the ripening (aging) process, cheesemakers sometimes wash the rinds with brine. By using the same liquid and the same cloth from one cheese to the next, they ensure the uniformity of the bacteria and fungi in all their cheeses.

Microflora will also be influenced by moisture, pH, salting, ripening temperature, etc.

But while part of the microflora is deliberately inoculated into the milk by the cheesemaker, a significant portion is also naturally deposited on its surface.

And it's also what makes it so hard to maintain a consistent taste and quality of cheese. From one batch to the next, it takes just one change of season, one new source of spores or unwanted contamination for the taste of the product change.

These are variations that major dairies such as Agropur cannot afford. Agropur is a cooperative, owned by 3,400 dairy farmers that transforms more than a quarter of the milk produced in Canada.

In partnership with the cooperative, Steve Labrie’s project aims to develop a genetic tool that can better control the production of cheese, limit losses and produce high quality cheeses that will have a longer shelf life and will result in fewer returns.

“This is what gives regional products their special character,” Labrie says. “The fungi spores and bacteria that float in the air in one region of the country are not the same as those in another. This is what makes it almost impossible to copy a cheese that is produced somewhere else.”

“Furthermore,” he says, “the project will create a set of standardized genomic profiles for each cheese, a kind of checklist that can be used in the factory to ensure that the aging process of each cheese follows its normal course.”

“There are many more bacteria than previously thought and classical biology is not up to the task of understanding these microflora. Modern genomics and informatics will help us reach that goal.”

In the meantime, the researcher’s laboratories will continue to be redolent with the odour of cheese. The various active genes on a cheese are mapped by high-throughput sequencing, and the species present are determined. The next step is to understand the metabolic activities involved.

“You must never forget that microbes influence each other. A cheese is more than the sum of the bacteria and fungi it’s made up of. New flavors can emerge from the meeting of two or more organisms.”

With his team, Labrie deliberately produces spoiled cheeses and sequences the genome of their microflora. By comparing their profiles to the desired profiles, he is beginning to understand how much impact variations in manufacturing parameters can have.

“In the past, it was estimated that around 150 different species could develop on a specialty cheese, not counting the many strains of each species,” Labrie says.“With today’s genetic tools, we realize that this number was greatly underestimated.”

In the end, when the researcher has characterized the ripening process of all the Agropur cheeses, he will hand the genetic tools he has developed over to the cooperative so that it can conduct the tests itself, and continue to provide us with more assurance than ever before, with high-quality specialty cheeses.